Calculating population genetic statistics from VCF files using BCFtools

popstats_from_vcf.Md

Useful Oneliners for Calculating Population Genetic Statistics from VCF files

The following commands require non-standard software like BCFtools and VCFtools.

thin variants to prevent linkage biases and output the number of sampled alleles and the allele frequency for the reference allele

vcftools --thin 10000 --recode --recode-INFO-all --stdout --gzvcf <my_variants.vcf.gz> | \
  bcftools query -f '%CHROM\t%POS[\t%GT]\n' - | \
  awk -v OFS="\t" '{ miss=0; hom_ref=0; hom_alt=0; het=0; \
    for (i=3; i<=NF; i++) \
    if ($i == "./.") miss += 1; \
    else if ($i == "0/0") hom_ref += 1; \
    else if ($i == "1/1") hom_alt += 1; \
    else if ($i == "0/1" || $i == "1/0") het += 1; \
    pres=hom_ref+hom_alt+het; \
    print $1, $2, pres*2, ((2*hom_ref)+het)/(2*pres) }'